They said they would review the incident and work together in the future to fight terrorism and drug-trafficking.
Venezuela had accused Colombia of violating its sovereignty by paying bounty-hunters to seize the commander, Rodrigo Granda, in its territory.
It cut off commercial links and suspended a $200m gas pipeline project.
Venezuela also withdrew its ambassador from Bogota – a gesture not reciprocated by Colombia.
Colombia initially denied claims it had abducted Commander Granda, a member of the left-wing Farc, from foreign soil but later admitted paying bounty hunters to secure his capture.
Venezuela demanded an apology from Colombia over the capture.